Protected areas are one of the main tools for biological conservation worldwide. Although they have contributed to an increase in fish abundance and alleviated the impacts of fishing on marine ecosystems, the impacts of fishing and of protected areas in freshwater ecosystems are less well known. We compared fishing productivity and fish assemblage descriptors of two distinct protected areas designated for sustainable use of natural resources and an unprotected area in the Tapajós River, in the Brazilian Amazon. Two hypotheses were tested: (1) fishers from protected areas have higher catch per unit effort than those from unprotected areas; and (2) fish assemblages in protected areas have higher biomass, abundance, presence of target species, species richness, fish size and mean trophic level than those in unprotected areas. A total of 2,013 fish landings were recorded and two surveys were undertaken to sample fishes. Eleven environmental parameters were quantified to distinguish between effects of environmental heterogeneity and protected areas. The catch per unit effort of fishers was higher within protected areas than in unprotected areas, suggesting that protected areas reduce the levels of fishing pressure and increase fishing productivity. However, the fish assemblage descriptors were correlated more with environmental variables than with protected areas, indicating a relatively weak effect of protected areas on fish communities in lakes. The results highlight the importance of considering the influence of environmental heterogeneity in fish conservation programmes, and the positive effect of protected areas on fishing productivity in freshwater environments.